Methods and systems for detecting entities in a biological sample

ABSTRACT

Apparatus and methods for use with a blood sample are described. The blood sample is stained with a first dye that predominantly stains DNA, and a second dye that stains at least one other cellular component being different from DNA. A plurality of images of the blood sample are acquired. A candidate object is identified as being a candidate of a given entity. A first stained area, which is stained by the first dye and which is disposed within the candidate object, is identified. A second stained area, which is stained by the second dye and which is disposed within the candidate object, is identified. The entity is detected by determining that features of the stained areas satisfy predetermined criteria associated with the entity. Other applications are also described.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.16/705,941 to Pollak (published as US 2020/0181680), filed Dec. 6, 2019,which is a continuation of U.S. patent application Ser. No. 14/369,251to Pollak (issued as U.S. Pat. No. 10,640,807), filed Jun. 27, 2014,which is a US national phase application of PCT Application No.PCT/IL/2012/050556 to Pollak (published as WO 13/098821), filed Dec. 27,2012, which claims the benefit of:

PCT Application No. PCT/2011/000973 to Bachelet (published as WO12/090198), filed Dec. 29, 2011; and

U.S. Provisional Application No. 61/664,769 to Pollak, filed Jun. 27,2012.

TECHNOLOGICAL FIELD

The present disclosure concerns diagnostic methods and in particular,methods and systems for detecting pathogens in bodily fluids.

BACKGROUND

Staining is a technique frequently used in biology and medicine tohighlight structures in biological tissues for viewing, often with theaid of different microscopes. Stains may be used to define and examinebulk tissues (highlighting, for example, muscle fibers or connectivetissue), cell populations (classifying different blood cells, forinstance), or organelles within individual cells.

Cell staining is used to better visualize cells and cell componentsunder a microscope. By using different stains, one can preferentiallystain certain cell components, such as a nucleus or a cell wall, or theentire cell. The stains can be used on fixed, or non-living cells, aswell as on living cells.

Cell staining techniques are also often used to detect a pathogen in ablood sample. One important pathogen is the malaria.

The first dye synthesized for detection by staining methylene blue, in1876. Six years later, it was used to discover tubercle bacillus. Withinthe years, modifications of MB were employed, including, “ripened” MB incombination with other dyes, such as eosin, which alloweddifferentiation between blood cells and the nuclei of malarialparasites, as well as the combination of MB methylene blue demethylationwith glycerol as a stabilizing agent in methanol solvent, known as theMalachowski-Wright-Giemsa stain.

J. Keiser et al. describe Acridine Orange in comparison to Giemsa stain,for malaria diagnosis, including its diagnostic performance, itspromotion and implementation and the implications for malaria control.

U.S. Pat. No. 5,470,751 describes another reagent for staining malariainfected cells and a method for detecting malaria infected cells usingthe same, wherein the reagent is a staining solution comprising at leastone first dye of an Auramine analogue, such as Auramine O and at leastone second dye of a condensed benzene derivative, such as3,3′-diethyl-2,2′-oxacarbocyanine iodide. A test sample is treated withreagent to stain malaria infected cells. The stained malaria infectedcells are then optically detected.

In addition, the Centers for Disease Control and Prevention CDC,Diagnostic Procedures, 2009 describes under the heading “Bloodspecimens: Microscopic Examination” the Kawamoto technique for thedetection of blood parasites, such as malaria parasites, usingfluorescent dyes that stain nucleic acids. As discussed in thispublication, in the Kawamoto technique, blood smears on a slide arestained with acridine orange (AO) and examined with either afluorescence microscope or a light microscope adapted with aninterference filter system. This results in a differential staining ofnuclear DNA in green and of cytoplasmic RNA in red, which allowsrecognition of the parasites.

GENERAL DESCRIPTION

The present disclosure provides, in accordance with a first of itsaspects, a method of detecting a pathogen infection in a sample, themethod comprising:

-   -   staining said bodily sample with two or more dyes, comprising at        least one dye predominantly staining DNA to thereby provide        differential staining between DNA and at least one other        cellular component being different from DNA;    -   identifying at least a first stained area comprising the DNA, if        exists in the sample, and at least one other stained area        comprising the other cellular component;    -   extracting structural features for the first stained area and        the at least one other stained area, said structural features        comprise at least one of (i) size of at least one of the first        stained area and one other stained area and (ii) location of        said first stained area and said at least one other stained area        one with respect to the other; and    -   determining the presence of a suspected pathogen in the sample        if a first stained area was identified and said structural        features conform to structural features predetermined as        characterizing the suspected pathogen.

In accordance with a second aspect, the present disclosure provides akit comprising:

-   -   a first dye predominantly staining DNA;    -   a second dye for staining at least one other cellular component        being different from DNA;    -   instructions for use of said first dye and said second dye in        determining presence of a suspected pathogen in a sample.

In accordance with a third aspect, the present disclosure provides asystem comprising:

-   -   an image capturing component configured and operable to acquire        at least one optical image of a stained area in a sample, the        stained area comprising a first stained area corresponding        predominantly to DNA and at least one other stained area        corresponding to at least one other cellular component being        different from DNA;    -   an image processing unit configured to    -   i) extract structural features of said at least first stained        area and said one other stained area, said structural features        comprise at least one of (i) size of at least one of said first        stained area, and (ii) one other stained area; and a location of        said first stained area and said one other stained area one with        respect to the other; and    -   ii) determine the presence of a suspected pathogen in the bodily        sample, if a first stained area is identified and said        structural features conform to structural features predetermined        as characterizing a pathogen infection.

Yet, in accordance with a fourth aspect, the present disclosure providesa processing unit for identifying a pathogen in a sample, comprising:

-   -   input module configured and operable to receive data        corresponding to a stained object in the sample comprising at        least a first stained area corresponding predominantly to DNA        and at least one other stained area corresponding to at least        one other cellular component being different from DNA, and    -   an image processing unit configured and operable to process said        data corresponding to said stained object, the processing        comprises:    -   extracting structural features for the at least the first        stained area and second stain area in the stained object, said        structural features comprise at least one of (i) area of at        least one of the first and the one other stained area and (ii) a        location of said first stained area and said one other stained        area one with respect to the other; and    -   providing a value or combination of values being indicative of        the presence or absence of a suspected pathogen in the sample,        if said structural features conform to structural features        predetermined as characterizing the suspected pathogen

In accordance with a fifth aspect, the present disclosure provides acomputer program product comprising a computer useable medium havingcomputer readable program code embodied therein for detecting a pathogeninfection in a sample being stained with two or more dyes, the computerprogram product comprising:

computer readable program code for causing the computer to identify inthe stained object at least a first stained area correspondingpredominantly to DNA and at least one other stained area correspondingto at least one other cellular component being different from DNA;

computer readable program code for causing the computer to extractstructural features for the at least a first stained area and one otherstain area, said structural features comprise at least one of (i) areaof at least one of the first and one other stained areas and (ii)location of said first stained area and said one other stained area onewith respect to the other;

computer readable program code for causing the computer to determine avalue or combination of values being indicative of the presence of asuspected pathogen in the sample if said structural features conform tostructural features predetermined as characterizing the suspectedpathogen infection.

BRIEF DESCRIPTION OF THE DRAWINGS

In order to better understand the subject matter that is disclosedherein and to exemplify how it may be carried out in practice,embodiments will now be described, by way of non-limiting example only,with reference to the accompanying drawings, in which:

FIGS. 1A-1F show images obtained at three different exposures; thebright field (FIGS. 1A, 1D), blue fluorescence (365 nm, FIGS. 1B and 1E)and UV fluorescence (475 nm, FIGS. 1C, 1F) images of white blood cells(FIGS. 1A-1C) and malaria infected red blood cells (FIGS. 1D-1F).

DETAILED DESCRIPTION OF EMBODIMENTS

The present invention is based on the development of methods fordifferential stain different components in a blood sample to therebyallow an almost instant detection of an infection in the blood.

Specifically, it has been found by the inventors that staining of ablood sample with acridine orange (AO) reagent allows differentiationbetween DNA containing pathogens and, for example, platelets,reticulocytes, Howell-Jolly bodies, and bacteria such as Staphylococcusepidermidis.

It has been further found that staining of a blood sample with AO andHoechst reagents and by employing an image analysis of the stainedobject including the two different stained areas (the object being animage in the field of view comprising the stained areas underexamination), allowed detection of malaria infection in the bloodsample. In this connection, the inventors have found that in addition todetecting two different stained areas in the viewed stained object (ofthe sample), it is sometimes also important to take into considerationsome spatial features of the stained areas, such as the size ordimensions of each stained area and/or the spatial relationshiptherebetween.

The inventors have also determined that in order to detect a pathogen inthe blood sample, at least one dye should stain deoxyribonucleic nucleicacid (DNA) with preference over staining of other cellular components.

It has been further found by the inventors that the diagnosticsensitivity obtained by using two dyes, one predominantly staining DNA,is above 95%, and even above 97% or 99%.

Further, it has been found, and was also shown in the following example,that the method disclosed herein allows identifying the presence of apathogen at low counts/μl. For example, the example provided hereinshows that a parasite, such as Plasmodium may be detected in the bloodeven at a count below 1,000 parasites per μl and even at a low count ofabout 20 parasites per μl.

Thus, in accordance with a first aspect, the present disclosure providesa method of detecting a pathogen infection in a sample, the methodcomprising:

-   -   staining said bodily sample with two or more dyes, with at least        one dye predominantly staining DNA to thereby provide        differential staining between DNA and at least one other        cellular component, being different from DNA;    -   identifying at least a first stained area comprising the DNA, if        exists in the sample and at least one other stained area        comprising the other cellular component;    -   extracting spatial features for the first stained area and the        at least one other stained area, said spatial features comprise        at least one of: (i) size of at least one of the first stained        area and one other stained area; and (ii) location of the first        stained area and the at least one other stained area one with        respect to the other;    -   determining the presence of a pathogen in the sample if a first        stained area was identified and said spatial features conform to        (namely, matches, corresponds to, falls within, is associated        with), a value or a combination of values predetermined as        characterizing a suspected pathogen infection.

As appreciated, while the invention is described in the followingdetailed description with reference to a method of detecting a pathogeninfection in a sample, such as a blood sample, it is to be understoodthat the present disclosure also encompass a kit for performing theinvention, a system, a processing unit and other aspects, as disclosedherein,

The method of the invention is applicable for a variety of samples. Insome embodiments, the sample is a bodily sample. In some embodiments,the bodily sample is a fluid bodily sample such as, without beinglimited thereto, blood, saliva, semen, sweat, sputum, vaginal fluid,stool, breast milk, bronchoalveolar lavage, gastric lavage, tears andnasal discharge.

In some embodiments, the bodily sample is a blood sample.

In some embodiments, the blood sample is selected from whole bloodsample, red blood cell sample, buffy coat sample, plasma sample, serumsample, a sample from any other blood fraction, or any combinationthereof.

The bodily sample may be from any living creature but preferably fromwarm blooded animals.

In some embodiments, the bodily sample is a sample from a mammal.

In some embodiments, the bodily sample is one taken from a human body.

In some other embodiments, the sample is taken from any domestic animal,zoo animals and farm animals, including but not limited to dogs, cats,horses, cows and sheep.

In some embodiments, the bodily sample may be taken from animals thatact as disease vectors including deer or rats.

In some other embodiments, the sample is an environmental sample, suchas, without being limited thereto water (e.g. groundwater) sample,surface swab, soil sample, air sample, or any combination thereof.

In some embodiments, the sample is a food sample, such as, without beinglimited thereto, meat sample, dairy sample, water sample, wash-liquidsample, beverage sample, and any combination thereof.

As a first stage in the method disclosed herein, the sample is stainedwith at least two dyes providing, under suitable conditions, twodistinct stained areas in the sample.

A stained area may be defined, inter alia, with respect to, for example,background or collateral staining. For example, an intensity-basedthreshold, contrast-based threshold, edge detection, backgroundsubtraction, normalization, or combination thereof may be applied todefine the stained area. Additionally, the definition of stained areamay allow, inter alia, for diffuse boundaries, for example, by using abrightness-weighted sum/integral.

In some embodiments, such as in the case of membrane staining, a firststained area residing within a second stained area may be defined toinclude a case wherein the first area resides within the areacircumscribed within the second area. For example, membrane staining ofred blood cells may result in a second stained area that resemblesnarrow lines around the circumference of the cell (as viewed in atwo-dimensional microscope image); in such a case, it may be determinedthat the first area resides within said second area if it falls withinthe stained cell circumference.

In some embodiments, standard microscopic sample preparation may berequired for staining the sample. For example, sample preparation maytake advantage of the well-known thin smear or thick smear method forblood smear preparation. As an alternative example, a drop of the sampleis placed in the middle of a clean slide together with, before or afterplacing the dye and a cover slip is gently placed over the drop at anangle, with one edge touching the slide first. The liquid is thenallowed to spread out between the two pieces of glass without applyingpressure.

When referring to a dye it is to be understood as encompassing anychemical or biological substance that is capable of staining a componentof a biological cell, to enhance contract and highlight structures ofthe stained object, be it a cell or part of a cell. The dye may have aclass preference or specificity, e.g. may have preference or specificityto staining of nucleic acids and among the nucleic acid, to DNA or RNA,preference or specificity to amino acids, to lipids, carbohydrates etc.

When referring to preference or predominant staining it is to beunderstood that the dye stains one other cellular component in aparticular color or fluorescence that is at least twice, three times,four times or even 10 times greater in its intensity than its stainingintensity to another cellular component at that same color orfluorescence spectrum.

In some embodiments, when referring to preference or predominantstaining it is to be understood that the dye has affinity (molecularattraction) to one cellular component (in the particular color orfluorescence spectrum) that is at least twice, three times, four timesor even 10 times greater in its affinity to another cellular component(at that same color or fluorescence spectrum).

In some further embodiments, when referring to preference or predominantstaining it is to be understood that the staining of DNA by the dye isstable or has more stability as compared to its staining of othercomponents. Stability may be understood to mean that the stainingproduced by the dye remains substantially consistent for at least 30minutes after being brought into contact with the dye, at times, atleast 1 hour, 2 hours or even 5 hours after staining the sample with thedye having preference to DNA. Alternatively, stability may be understoodto mean that the staining produced by the dye remains substantiallyconsistent during exposure to light (e.g. light used for fluorescenceexcitation) for at least 0.25 seconds, 1 second, or even 15 seconds ofexposure.

In this context, it is to be understood that the dye having preferenceto DNA may also stain other cellular components but with lowerattraction or lower intensity or with a different florescence response(excitation spectrum and/or emission spectrum) such that it allows thegreater enhancement of the DNA, which the dye has preference. Forexample, as will be further discussed below, under some conditions a dyemay predominantly stain DNA, however, under some other conditions, thesame dye may stain RNA.

Similarly, the staining of one other cellular component should beunderstood as encompassing staining of one or more cellular componentsother than DNA. This may also include staining of one or more cellularcomponents in addition to DNA, but with no preference or lowerpreference to staining of DNA.

In some embodiments, the dyes are not cell type specific. In otherwords, the dye is not specific to a particular pathogen or to aparticular stage of the life cycle of a particular pathogen or to aparticular cell of the host being infected therewith and will stain acell component irrespective of its origin, e.g. a DNA sequence orstructure per se, an RNA sequence or structure per se, protein per se,etc.

The existence of a first stained area is determined based on variousfactors that may relate, inter alia, to the intensity of the stain, theshape of the stain, the variability or consistency of the stain etc.Once a first stained area is determined to exist, it is ascribed to thepresence of DNA.

The method also provides a stained area of at least one other cellcomponent being different from DNA. The stained area may be obtainedfrom the same dye, under different conditions or by the use of adifferent dye.

Without being limited thereto, the at least one other cellular componentis selected from the group consisting of RNA, proteins, lipids,membrane, cytoplasm, ribosomes, carbohydrates, glucans, glycoproteins,endoplasmatic reticuli, or any combination thereof.

In some embodiments, the at least one other cellular component is RNA.

There are a variety of dyes that may be used in accordance with thepresent disclosure. In some embodiments, the dye is a chromophore orfluorophore.

Dyes such as the Giemsa stain are known as chromogenic—their effect isto provide color or opacity to the sample and are visible, for example,in bright field microscopy.

In some embodiments, the dye provides fluorescent staining of thesample. Fluorescence is visualized by illuminating the sample with an“excitation” spectrum of light, which results in an “emission” at adistinct spectrum of light. Amongst the potential advantages offluorescent stains is that the regions of the sample that are notstained show up as dark or nearly dark, thereby typically providinggreater contrast between stained and unstained areas than chromogenicstains. Acridine Orange (AO) is an example of a dye used to fluorescentstaining of biological samples.

In some embodiments, the dye is a cell permeating dye.

Without being limited thereto, a dye that predominantly stains DNA maybe any member of the group consisting of acridine orange (AO,N,N,N′,N′-Tetramethylacridine-3,6-diamine, green staining), Hoechstfamily, DAPI (4′,6-diamidino-2-phenylindole), ethidium bromide(3,8-Diamino-5-ethyl-6-phenylphenanthridinium bromide), propidium iodide(2,7-Diamino-9-phenyl-10 (diethylaminopropyl)-phenanthridium iodidemethiodide), SYBR family, YOYO, DRAQ family, SYTO family, TOTO family,or any combination thereof. Additionally the dye comprises a chemicalmodification of any of the aforementioned dyes that preserves its DNApreference.

Without being limited thereto, a dye that does not predominantly stainDNA may be any member of the group consisting of crystal violet(Tris(4-(dimethylamino)phenyl)methylium chloride), Hematoxylin stains,eosin stains, Safranin (azonium compounds of symmetrical2,8-dimethyl-3,7-diamino-phenazine), acridine orange (AO,N,N,N′,N′-Tetramethylacridine-3,6-diamine, red staining), acid-Schiffstains, Masson's stain, Prussian blue, or any component or combinationthereof. Many more stains that do not predominantly stain DNA are knownin the art.

Dyes such as AO provide different fluorescence spectra for differentcellular components. When AO stains DNA at neutral pH, it has anexcitation maximum at 502 nm (cyan) and an emission maximum at 525 nm(green); when it stains RNA at neutral pH, the excitation maximum shiftsto 460 nm (blue) and the emission maximum shifts to 650 nm (red). Assuch, it allows differential staining between DNA and RNA, depending onthe excitation wavelength and conditions of the sample.

The Hoechst family of dyes are known by the chemical formula C₂₅H₂₆N₆R,with R representing a variety of possible substituents, such as, withoutbeing limited thereto, —OH (Hoechst 33258); —CH₂CH₃ (Hoechst 33342),—N(CH₃)₂ (Hoechst 34580), —SO₂NH₂ (Hoechst S769121).

In some embodiments, the method involves the combined staining with atleast two dyes, the first dye being a member of the Hoechst family andthe second dye being acridine orange.

When referring to a combination of two or more stains, it is to beappreciated that the two or more dyes may be added to the samplesimultaneously or in sequence. Similarly, the respective stained areasmay be obtained simultaneously or in sequence, as long as there is atime point that allows viewing two or more differently stained areas inthe same sample.

In one embodiment, the method employs a combination of AO with themembrane-permeable dye that is essentially specific to nuclear DNA (e.g.Hoechst 33342, yielding a blue emission).

According to this embodiment, AO allows using the red-emission or acombination of the green and red emissions to stain the pathogen'scytoplasm (and possibly also the nucleus, but without substantiallyinterfering with the Hoechst staining).

In some embodiments, the combination of AO and Hoechst allows thedetection of a parasite. According to this embodiment and without beinglimited thereto, for the detection of a parasite, such as a member ofthe Plasmodium species, the concentration of Hoechst reagent such asHoechst 33342 may be 10 μg/mL, but other possible values may be used aswell, for example in the range between 3 μg/mL and 250 μg/mL; and AO maybe used at 1.5 μg/mL, but other possible values may be used as well, forexample in the range between 0.2 μg/mL and 125 μg/mL.

In some embodiments, the amount of AO and Hoechst reagent to be used isdetermined so as to provide, in the biological sample, a ratiotherebetween. Accordingly, the Hoechst:AO ratio may be in the range ofbetween 50:1 to 1:1, at times, about 7.5:1.

A same or similar ratio may also be applicable for other dyecombinations, a first dye staining predominantly DNA and the other dye,one other component, as defined, namely, a ratio between the first dyeand other dye in the range of between 50:1 to 1:1.

AO may additionally or alternatively be used to stain, for example,Plasmodium cytoplasm and/or food vacuole, but not the cytoplasm of thered blood cell (RBC) that the parasite may be inside, allowing theparasite's body to be seen without being obscured by an RBC even ifpresent within the RBC.

Appropriate concentrations may be optimized with respect to factors suchas the particular dye combination, desired duration of stain incubation,brightness of resulting color or fluorescence, and character of theresulting staining.

In some embodiments, the method disclosed herein is applicable for thedetection of an infection by a DNA-carrying pathogen. As such, at leastthe first dye stains at least the DNA, if present in the sample tothereby provide a first stained area indicative of the presence of theDNA carrying pathogen in the sample.

The pathogen may be any infectious microorganism. In some embodiments,the pathogen is a eukaryotic parasite. When referring to eukaryoticparasite, in the context of the present disclosure, it is to beunderstood as encompassing one cell parasites and multicellularparasites but also fungi, such as yeast (e.g. Candida) and Aspergillus.

In some embodiments, the pathogens are bacteria. This includes, forexample and without being limited thereto, Escherichia coli,Staphylococcus aureus, Microbacterium tuberculosis, Salmonella species,Borrelia species and Treponema pallidum and others known.

In some embodiments, the pathogen is a eukaryotic parasite. Inaccordance with this embodiment, the parasite may be a one cellparasite, such as protozoa. This includes genital protozoa, e.g.Trichomonas vaginalis, nervous system protozoa, e.g. Naegleria fowlerifecal protozoa, e.g. Giardia lamblia, blood protozoa. In someembodiments, the pathogen may be a multicellular parasite, such asWuchereria bancrofti, Brugia malayi, Brugia timori, Mansonellastreptocerca, or Onchocerca volvulus.

In some embodiments, the parasite is a blood protozoa selected from thegenuses consisting of Trypanosoma (causing Chagas disease and Africansleeping sickness); Plasmodium (causing Malaria); Toxoplasma (causingToxoplasmosis); Babesia (causing Babesiosis).

Specifically, when referring to Plasmodium it is to be understood asencompassing at least any member of the group consisting of Plasmodiumfalciparum (P. falciparum), Plasmodium vivax (P. vivax), Plasmodiumovale (P. ovale), Plasmodium malariae (P. malariae), and Plasmodiumknowlesi (P. knowlesi).

In some embodiments, pathogen is understood to mean a particular stageof the life cycle of a particular pathogen or group thereof. Forexample, the invention disclosed herein can be applied specifically tothe detection of trophozoites, schizonts or gametocytes of Plasmodiumspecies or P. falciparum in particular.

As may be appreciated, the method disclosed herein may be applicable forthe detection of multiple pathogens using the same conditions and/or inthe same sample, e.g. same combination of dyes, same test conditionsetc., as well as for the detection of a pathogen at multiple stages ofits life cycle. In some embodiments, the method disclosed herein maydetermine which one or more of the multiple pathogens (or life stages)is suspected.

In some embodiments, the method disclosed herein is for detectingPlasmodium infection in a human blood sample, the method comprising:

-   -   staining the human blood sample with at least two dyes, under        conditions that allow at least staining of DNA and at least one        other cellular component being different from DNA;    -   identifying at least a first stained area comprising the DNA, if        exists in the blood sample, and at least one other stained area        comprising one other cellular component in the blood sample;    -   extracting structural features for the first stained area and        the at least one other stained area, said spatial features        comprising size of at least one of the first stained area and        one other stained area and a location of the first stained area        and the at least one other stained area one with respect to the        other;    -   determining value or combination of values being indicative of        the presence of suspected Plasmodium in the blood if a first        stained area was identified and said structural features fall        within limitations predetermined as characterizing a pathogen        infection.

In some embodiments relating to determination of the presence ofPlasmodium in the blood, the stained object is obtained by staining theblood sample with a combination of acridine orange (AO) and Hoechst dye,in particular, Hoechst 33342 with a concentration ratio between AO andHoechst 33342 in the range of 1:50 and 1:1, at times, even in the rangeof 1:7.5.

In accordance with the above embodiment, the method is applicable fordetection of malaria infection in a human blood sample.

Once the sample is stained with the one or more dyes, at least onestained object is obtained and the method then involves selecting atleast one stained object in the sample and obtaining structural orspatial features of the stained object.

When referring to spatial or structural features of a stained object itis to be understood as encompassing any measurable feature of thestained areas in the selected stained object. The features may bepresented as a discrete value or as a range of values characterizing thestained area.

In some embodiments, the structural features include at least one of thesize (e.g. dimension, length, circumference, minimum width, maximumwidth, or area) of the stained areas and/or the location of the firststained area with respect to the location of the other stained area orareas. In other words, the method may be performed based at least oneeither determining dimensions, e.g. area of the stained areas, or on thelocation of the first stained area with respect to the location of theother stained area or areas. These features may be combined also withone or more additional features.

The additional structural features may include, without being limitedthereto, shape of stained area(s), pattern of movement of stainedarea(s), intensity of stained area(s), color of stained area, texture(contour) of stained area, sharpness of boundary of stained area,pattern of staining in intensity or color, overlap of stained area withother stained areas or image features, relative size of stained area toother stained areas or image features, proximity or contact of stainedare to other stained areas or image features

In some embodiments, the bodily sample is a blood sample.

In some embodiments, the pathogen is a blood parasite.

In some embodiments, the bodily sample is human blood and the pathogenis Plasmodium species responsible for human malaria, such as thoseselected from the group consisting of P. falciparum, P. vivax, P. ovaleand P. malariae.

When the bodily sample is a blood sample, the extraction of structuralfeatures comprises selecting a stained object in the blood sample thatcomprises the first stained area and the at least one other stainedarea.

Based on the stained areas and the analysis of the structural features ahigh probability of the sample being infected with a suspected pathogenis determined. Thus, in the context of the present disclosure, whenreferring to determination of presence of a pathogen or suspectedpathogen it is to be understood that any one of the following isdetermined:

-   -   that one or more suspected pathogen are present in the sample;    -   that one or more suspected pathogens are present in the sample        at a confidence levels above a predefined threshold; the        confidence levels may increase or a final determination of the        presence of a suspected pathogen may require one or more        additional analysis steps.    -   that one or more suspected pathogens may be present in the        sample with a determined or estimated confidence scores or        probabilities that are available for additional analysis steps

In accordance with some embodiments, a suspected pathogen is determinedto be present in the sample if a first stained area is identified (beingindicative of the presence of DNA in the sample), and the first stainedarea abuts with, is in close proximity to, or resides within the oneother stained area and the size of at least one of the first stain, i.e.the DNA containing area, and of the one other stain is within apredetermined range. For example, a DNA containing area often lies nearan area stained for RNA, which exists in the cytoplasm.

In accordance with some other embodiments the suspected pathogen isdetermined to be present in the sample if a first stained area isidentified (again, being indicative of the presence of DNA in thesample) and the size of the first stained area satisfies a predeterminedrelation with respect to the size of the one stained area. Thiscriterion can be used, for example, to differentiate targeted eukaryoticparasites from bacteria: in eukaryotic cells, the area predominantlystained for DNA should be smaller than a cytoplasmic staining,indicating a distinct nucleus that is not present in bacteria.

In accordance with yet some embodiments, the presence of a suspectedpathogen is determined if a first stained area is identified and thedimensions or area of the first stained area is within a range of valuespredetermined to be associated with the particular pathogen or with aparticular stage of the life cycle of a particular pathogen. Forexample, if the pathogen is one causing malaria (i.e. Plasmodium), thearea of the first stained area would typically not be below 0.2 μm² orabove 20 μm² or would be in the range of 0.2 μm² to 20 μm². In someembodiments, the area of the first stained area in detection ofPlasmodium would not be below 0.8 μm² or above 13 μm² or would be withinthe range of 0.8 μm² to 13 μm².

In accordance with some other embodiments the presence of a suspectedpathogen is determined to be in the sample if a first stained area isidentified and the areas of the one other stained area are within arange of values predetermined to be associated with the particularpathogen or a particular stage of the life cycle of a particularpathogen. For example, if the pathogen is one causing malaria (i.e.Plasmodium), the area, for example, a cytoplasm, of the other stainedarea would typically not be below 0.8 μm² or above 65 μm² or would be inthe range of 0.8 μm² to 65 μm². In some embodiments for detectingmalaria infection, the area of the other stained area is not below 1.6μm² or does not exceed 40 μm² or is in the range of 1.6 μm² to 40 μm².

Considering the above features, it is understood that in accordance withsome embodiments of the present disclosure, particular area of the firststained area cannot exceed particular area of the one other stainedarea. Similarly, the dimensions of the first stained area should bestatistically significant (e.g. by t-test) smaller than the dimensionsof the other stained area.

In some other embodiments, the presence of a suspected pathogen isdetermined to be in the sample if a first stained area is identified andthe first stained area occupies a predetermined % volume of all theother stained areas. For example, when referring to malaria, the firststained area would typically occupy between 12% to 60% of said one otherstained area.

In accordance with some other embodiments the presence of a suspectedpathogen is determined to be in the sample if a first stained area isidentified and the first stained area and the one other stained areahave predetermined shapes. For example, the trypomastigote stage ofTrypanosoma brucei is known to have an elongated, rod like shape. Othershapes may include, without being limited thereto, spiral, oval,elongated and spherical properties.

In accordance with some embodiments, the presence of a suspectedpathogen is determined to be in the sample if a first stained area isidentified and the first stained area has a variability in intensitiesthat is above a predetermined threshold. The variability of intensitiesmay appear as a cluster of more than one area stained with the firststain (plurality of first stained area) or as an irregular shaped firststained area having different shades of color or fluorescence. This mayreflect, for example, a multinucleate stage in the development of aprotozoan, such as schizonts of Plasmodium.

Yet further, in accordance with some embodiments the presence of asuspected pathogen is determined if a first stained area is identifiedand the pattern of movement directionality and/or velocity) of thestained object corresponds with a pattern predetermined to be associateswith the suspected pathogen. For example, when considering Trypanosomabrucei, its motion (motility) is expected to occur at a characteristicpattern. As such, when the sample is stained with AO and Hoechststaining, the movement of the AO stained area may be analyzed to confirma match or an expected correlation with the expected pattern.

In yet some other embodiments, the presence of a suspected pathogen isdetermined if during movement of the stained object the first stainedarea is maintained within boundaries of the one other stained area.Thus, when referring to the above example with Trypanosoma brucei, themovement of the Hoechst stained area may be analyzed to ensure that aputative nucleus remains at all times within the moving AO stained area.

The structural features may be determined by simple viewing the sample,however, in some embodiments they are preferably determined based on oneor more optical images of the sample. Thus, in accordance with someembodiments, the method comprises capturing at least one optical imageof the stained object and extracting the structural features from the atleast one optical image.

At times, particularly when the structural parameter includes motion ormovement of the stained object, more than one optical image is capturedand the structural parameter of motion is determined based on a sequenceof images in time.

Needless that state, the more accumulated (or collected) information ofstructural parameter(s) of the stained object, the more accurate thedetermination and identification of a pathogen in the sample may be.

The structural features may be analyzed manually, or by the use of adedicated system for allowing an automated and as such, relatively fastdetection and/or identification of the pathogen in the bodily sample.The result of the analysis may retrieve a Yes/No indication of thepresence of a pathogen, a probabilistic indication of the presence of apathogen, images of a suspected pathogen for further analysis (manual orautomatic) and/or may provide a more specific result, including the typeof the pathogen, level of invention (count/μ1) etc.

The use of an automated system may be of significance, not only forovercoming human errors in analyzing the stained objects in the sampleand saving time and labor, but also since certain components of a bodilysample may not stain immediately and/or the degree of staining may varysignificantly over time, as is the case in sometimes with Hoechst 33342staining of blood contaminated cells. Consequently, imagecharacteristics may vary depending on how quickly the sample isanalyzed. As such, there is an advantage of having an automated systemallowing the rapid, or even almost instantaneous, imaging and analysisof the stained sample.

Thus, in accordance with a further aspect of the present disclosurethere is provided a system comprising:

-   -   an image capturing component configured and operable to capture        at least one optical image of a stained area in a sample, the        stained area comprising a first stained area corresponding        predominantly to DNA and at least one other stained area        corresponding to at least one other cellular component being        different from DNA;    -   an image processing unit configured to extract structural        features of said at least first stained area and said one other        stained area, said structural features comprising at least size        of at least one of said first stained area, and one other        stained area; and a location of the first stained area and said        one other stained area one with respect to the other; and        determine that a pathogen is present in the sample, if a first        stained area is identified and the structural features conform        to structural features predetermined as characterizing a        pathogen infection.

In some embodiments, the system also includes an output unit forproviding an output comprising a value or combination of values beingindicative of the presence or absence of suspected pathogens in thesample.

In some embodiments, the system is preferably computer-based using acollection of parameters being stored therein and corresponding to,inter alia, structural features associated with at least one definedpathogen. The parameters may, for example, include expected values orranges of values of the structural features, associated with a pathogen,or parameters that control the execution of machine-learning or dataanalysis algorithms. The parameters may be derived from informationgathered a priori or simultaneously obtained based on reference samplesincluding pre-determined pathogens.

The parameters may also comprise information relating to the behavior ofa pathogen, or cell infected with a pathogen, such as motility andvariations in features depending on the particular stage of the lifecycle of a particular pathogen.

The parameters may also comprise information regarding conditions to beused for the detection of a pathogen on a type of bodily sample, e.g. onblood sample, statistical information regarding the staining qualitiesand variability of a set of dyes to be used for a particular bodilyfluid, alternative dye combinations or condition combinations, etc.

In some embodiments, the collection of stored parameters comprisesparameters associated with a plurality of pathogens. In someembodiments, the collection of stored parameters comprises parametersthat associated with determining which one or more pathogens issuspected.

In some embodiments, the collection of parameters is associated withblood borne pathogens. In some other embodiments, the collection ofparameters is associated with blood parasites. In some particularembodiments, the collection of parameters is associated with pathogensthat harbor the human blood, in particular, of a Plasmodium speciesresponsible for human malaria, such as those selected from the groupconsisting of P. falciparum, P. vivax, P. ovale and P. malariae.

Further provided by the present disclosure is an image processing unitfor identifying a pathogen in a sample, comprising:

-   -   input module configured and operable to receive (image) data        corresponding to the stained object in the sample comprising at        least a first stained area corresponding predominantly to DNA        and at least one other stained area corresponding to at least        one other cellular component different from DNA, and    -   an image processing unit configured and operable to process the        data corresponding to the stained object, the processing        comprises:        -   extracting structural features for the at least the first            stained area and the one other stained area in the stained            object, said structural features comprising at least one            of (i) size of at least one of the first and the one other            stained areas and (ii) location of said first stained area            and said one other stained area one with respect to the            other; and        -   providing a value or combination of values being indicative            of the presence or absence of a pathogen in the sample, if            said structural features conform to structural features            predetermined as characterizing a suspected pathogen.

Several modes of operation may be used with respect to the system andimage processing unit. Automated as well as manual and semi-automatedsystems can be employed.

With respect to the system, the image capturing component may be anydevice configured and operable to acquire at least one optical image ofthe stained object being selected, for example, a CCD or CMOS camera.The image capturing component may be equipped with conventionalfunctionalities, such as focus functionalities. The image capturingcomponent may also include lenses, aperture and shutter.

The image capturing component provides image data for processing by theimage processing unit. The image data in the context of image analysisis based on a collection of pixel information that essentially coversone or more Regions of Interest (ROI).

The image data typically including the pixel information may bepresented in any available format, including, without being limitedthereto, Tagged Image File Format (TIFF), Joint Photographic ExpertsGroup (JPEG), Graphic Image Format (GIF), Portable Network Graphics(PNG), Portable Document Format (PDF), bitmap (BMP), and rawimage-sensor data. Image data can be in a compressed data format or inan uncompressed data format; may relate to any gray or color scale; caninclude bitmap data, or a portion of a bitmap file containing bitmapdata.

Once one or more images are captured, they are processed by the imageprocessing unit. The processing by the processing unit is configured andoperable to provide one or more values of structural features of thestained areas. In other words, based on image analysis techniques,various output values relating to structural features of the stainedareas are determined, which may allow the identification of the presenceor absence of the suspected pathogen in the sample or estimation of theprobability of presence therein. The values may include the dimensionsof one or more other stained areas in the ROI, the relationship betweenthe stained areas, and/or averages, compounding or statistics of valuespertaining to structural features. The processing may include, in someembodiments, analyzing the one or more values or combination of valuescorresponding to structural features with respect to the parameters(e.g. values or ranges of values or appropriate machine-learningweights) that have been a priori determined for characterizing one ormore pathogens, or differences therebetween.

The image analysis can be based on one or more of the common practicessuch as contour detection, image parameter derivatives, shape detection,image reconstruction, segmentation, image differencing, patternmatching, matched filtering, machine learning and geometric hashing.

Data processing by the image processing unit may use a classificationmodule. The classification module can be provided with at least onestructural parameter previously determined for a pathogen. Theclassification module can analyze the structural features provided anddeduce a selection of possible pathogens being identified. By way of anillustration, a classifier can identify a plurality of possiblepathogens or a single type of pathogen.

In particular embodiments, the structural features determined areassociated to an expected pathogen and these are analyzed with respectto the pre-defined parameters.

It should be noted that the identification of a single pathogen may be acomplex process which includes different combinations of features.Therefore, structural features determined following the use of aparticular combination of dyes can be used as criteria for subsequentanalysis of a further combination of dyes. For example, structuralfeatures identified in a previous analysis can be used to continue theidentification process while focusing of a subset of possiblecombination of dyes. For example, in a biological family level ofidentification of a pathogen, the results of previous analysis mayprovide a list of possible best filter(s) selection to be used in a nextround of analysis.

In some embodiments, image analysis and determination of the presence ofsuspected pathogens or a value or values indicative with the presence ofsuspected pathogens can take advantage of one or more machine-learningalgorithms, which operate on a plurality of structural features orrelated values. Such algorithms include without limitation SupportVector Machines (SVM), Artificial neural networks, Naive Bayesclassifiers, Bayesian networks, Decision trees, Nearest NeighborAlgorithms, Random Forests, Boosting, Regression analysis, Linearclassifiers, Quadratic classifiers, k-nearest neighbor, Hidden Markovmodels and any combination thereof. The result of the one or moremachine-learning algorithms can comprise one or more confidence score,probabilities and/or yes/no decisions.

As appreciated, the more features determined in the analysis—the moreprecise is the identification process. By using a plurality of dyes toinduce a plurality of structural features, the risk for misdetection ormisclassification is reduced. However, added features may alsocorrespond to increased computational or operational load. Someembodiments strive to balance the added benefit of added features withthe associate load drawbacks.

Based on the value or combination of values obtained by the analysis,various decisions are made by the processing unit as to the presence orabsence of a pathogen in the sample, including, at times, the type ofthe pathogen (qualitative identification) and/or the amount(quantitative identification) of the pathogen in the sample.

The processing unit is also configured to communicate with an outputunit. Thus, based on the output value or values of the structuralfeatures determined by the processing unit, an output signal or outputsignals indicative of presence or absence of at least one pathogen andin some embodiments, the type of the pathogen, in the acquired image isprovided by an output unit.

The output may be provided in any acceptable form, including a graph,graphic or text displayed on a monitor of a control unit, a printout, asa voice message, or a user's smartphone display, for accepting processeddata from the processing utility and displaying information relating tothe structural features obtained and/or associated values determiningthe presence and optionally the identity of a pathogenic infection,using, lists, tables, graphs etc. A monitor may be connected to aprinter for printing the output.

The processing unit may also include a user interface module, e.g. akeyboard, or a touch screen for allowing a practitioner, performing themethod of some embodiments of the invention, to control the operation ofthe system, including, inter alia, input data with respect to theexamined bodily fluid source, date, place, etc.) conditions of operatingthe system, types of dyes used, number of images to be taken, timeinterval between images, etc.

At times, image analysis may also involve adjustment or normalization ofimage brightness on the basis of degree of staining of the sample. Thesemay be based on, for example, identifying one or more of brightestand/or dimmest pixel values in the image or set of image (for example,corresponding to a particular sample), average brightness of brightestand/or dimmest area, and/or image histogram. Such features may beextracted from a representative image (not necessarily the one beingnormalized) or from statistical analysis of multiple images. Thefeatures used for normalization may be based on a single or multipleimages, which may be captured using different excitation wavelengths (asin AO providing different colors under different illuminationwavelengths).

Image brightness may also be adjusted using other control means, such asimage capturing component exposure time and/or brightness ofillumination.

Further, the conditions of operating the system may allow timing of theimage acquisition, e.g. to allow sufficient incubation time with the oneor more dyes as well as the operation with different opticalconfigurations of excitation and/or emission wavelengths, in order toimage the stained sample at various colors or fluorescence spectra.

In order to image the stained sample at various colors or fluorescencespectra, changes in excitation may be achieved by switching the color ofillumination. This can be done, for example, by providing two or morelight sources (e.g. for AO, UV LED light at 365 nm and blue LED light at475 nm) and combining them optically (for example, using a dichroicmirror or grating).

In another example, a single illumination source (e.g. UV LED light at365 nm) may be used to excite two dyes simultaneously, and one or moreoptical filters are moved in or out of the optical path to select therelevant emission wavelengths. Other dye sets can be simultaneouslyexcited using the same incident illumination as described here, even ifone or more of the dye is excited non-optimally. As an example, AO canbe similarly co-excited together with a Hoechst stain, DAPI and DRAQstains.

In yet another example, a single illumination source (e.g. UV LED lightat 365 nm) may be used to excite two or more dyes simultaneously, andthe emission optical path is split such that the two or more emissionsare captured on two or more image capturing components.

In yet another example, a color imaging sensor is used to simultaneouslycapture two or more fluoresce signals. Use of a color imaging sensorcan, for example, obviate the need for one or more optical filters thatare moved in or out of the optical path to select the relevantwavelength.

In the context of the present disclosure various illumination sourcesmay be used, these include, without being limited thereto, thoseproviding white light (as in bright light microscopy), UV light, bluelight, green light, yellow light, red light, combination thereof, or anylight applicable for exciting one or more of the dyes used for staining.

The components of the system, namely, the image capturing component, theprocessing unit, the output unit etc. may be directly connected to eachother (e.g. directly by a wire) or one or more of the components may beremote from one or more other components. For example, the imagecapturing device may send data to a processing unit over an intranet orover the internet, to allow processing at a remote location.

An example of a system which may be used for performing the method ofthe present disclosure is described in PCT patent applicationpublication No. WO 2012/090198, the content of which is incorporatedherein, in its entirety, by reference.

The processing unit is typically operable by running a dedicated programof instructions (e.g. software application) that performs the analysisand storage of incoming data. The software application may be embodiedin a program storage device readable by machine, such as a CD or memorydisk.

In line with the above, the present invention also provides a programstorage device readable by machine, tangibly embodying the program ofinstructions executable by the machine to perform the method disclosedherein, namely, a method of detecting a pathogen infection in a sample,the method comprising:

-   -   staining said fluid sample with two or more dyes, said two or        more dyes providing differential staining of at least DNA and at        least one other cellular component being different from DNA;    -   identifying at least a first stained area corresponding        predominantly to DNA and at least one other stained area        corresponding to the at least one other cellular component;    -   extracting structural features for the at least a first stained        area and the one other stain area, said structural features        comprising at least size of at least one of the first and one        other stained areas and a location of said first stained area        and said one other stained area one with respect to the other;    -   determining a value or combination of values being indicative of        the presence of a pathogen in the sample if said structural        features correspond to structural features predetermined as        characterizing a pathogen infection.

Yet further, the present disclosure provides a computer program productcomprising a computer useable medium having computer readable programcode embodied therein for detecting a pathogen infection in a bodilysample bodily sample being stained with two or more dyes, the computerprogram product comprising:

-   -   computer readable program code for causing the computer to        identify in a stained object within the bodily sample;    -   computer readable program code for causing the computer to        identify in the stained object at least a first stained area        corresponding predominantly to DNA and at least one other        stained area corresponding to at least one other cellular        component being different from DNA;    -   computer readable program code for causing the computer to        extract structural features for the at least a first stained        area and one other stain area, said structural features        comprising at least size of at least one of the first and one        other stained areas and a location of said first stained area        and said one other stained area one with respect to the other;    -   computer readable program code for causing the computer to        determine a value or combination of values being indicative of        the presence of a suspected pathogen in the sample if said        structural features correspond to structural features        predetermined as characterizing a pathogen infection.

Finally, the present disclosure provides a kit comprising:

-   -   a first dye predominantly staining DNA;    -   a second dye for staining at least one other cellular component        being different from DNA;    -   instructions for use of said first dye and second dye for        determining presence of a suspected pathogen in a bodily sample.

In accordance with this aspect, the first and second dye may be providedin a single composition or in a first composition comprising the firstdye and a second composition comprising the second dye. The first andsecond composition each comprising, in addition to the dye, a carriersuitable for use in staining the bodily sample with the respective dyes.

The kit disclosed herein is to be used for performing each of the stepsand conditions of the method disclosed herein.

In some embodiments, the first dye comprises a Hoechst dye. In someembodiments, the second dye comprises acridine orange.

In some embodiments, the kit comprises instructions for providing thebodily sample with the first dye and the second dye at a ratio the rangeof between 50:1 to 1:1.

In some embodiments, the first dye comprises Hoechst dye, specificallyHoechst 33342 and the second dye comprises AO, the concentration of thefirst dye is in the range between 3 μg/mL and 250 μg/mL; and theconcentration of AO is in the range between 0.2 μg/mL and 125 μg/mL.

In some other embodiments, the first dye comprises Hoechst dye,specifically Hoechst 33342 and the second dye comprises AO, theconcentration of the Hoechst 33342 is about 10 μg/mL and theconcentration of AO is about 1.5 μg/mL.

In some embodiments, the first and second dyes may be combined with asuitable buffer, such as, without being limited thereto one comprising1% Tris-EDTA buffer, 4.5% DDW and 92.5% saline.

Without wishing to be bound by theory, it is possible that theAO/Hoechst staining provided more robust and stable staining whichenabled rapid and efficient machine vision of the dyed sample. Thisallowed imaging of a greater amount of blood than may be examined undera microscope in conventional methods, which in turn provided highersensitivity at low parasitemia. It is also possible (in addition oralternatively) that one or more of the applied criteria of analysisprovided dependable results that are not dependent on the human factor.

Some embodiments of the present disclosure will now be exemplified inthe following description of non-limiting examples that were carried outin accordance with the disclosed method. It is to be understood thatthese examples are intended to be in the nature of illustration ratherthan of limitation. Obviously, many modifications and variations ofthese examples are possible in light of the above teaching. It istherefore, to be understood that within the scope of the appendedclaims, the invention may be practiced otherwise, in a myriad ofpossible ways, than as specifically described hereinbelow.

DESCRIPTION OF SOME NON-LIMITING EXAMPLES Detection of Plasmodium in aBlood Sample

A blood sample obtained from a human subject being identified as havingmalaria infection was stained with a dye solution comprising 2 μg/mlAcridine Orange, 15 μg/ml Hoechst 33342, 1% Tris-EDTA buffer, 4.5% DDWand 92.5% saline.

After staining, the samples were imaged using different color ofillumination, using UV LED light at 365 nm to image AO staining and blueLED light at 475 nm, to image the Hoechst staining) The sample was alsoimaged in the bright field (illuminating with white light).

The resulting images are provided in FIG. 1A-1F, with FIGS. 1A-1C beingobtained from a sample of white blood cells, and FIGS. 1D-1F beingobtained from the malaria infected red blood sample.

Specifically, FIG. 1A shows in the bright light field image, which showsthe boundaries (the membrane shown by the arrow in FIG. 1A) of a whitecell and that the DNA staining area (arrow in FIG. 1B) and of the othercomponent stained area (in this case the cytoplasm shown by the arrow inFIG. 1C) have dimensions that are typical to a white blood cell (bothDNA and RNA staining being larger than typical for a Plasmodiumparasite).

However, FIGS. 1D-1F show that first stained area (DNA, shown by thearrow FIG. 1E) and the second stained area (RNA, white spot in FIG. 1F)are much smaller than the boundaries of the cell (as shown by the arrowin FIG. 1D), being indicative of an infection of the anucleated redblood cell.

Notably, in a non-infected sample, no stained areas corresponding tothose shown in FIG. 1E and FIG. 1F are obtained.

These results show that by staining with at least two dyes, onepredominantly staining DNA (in this particular case Hoechst 33342) it ispossible to identify Plasmodium infection in a red blood cell.

Level of Confidence of Detection

In this study, a group of 200 blood samples was tested in accordancewith an embodiment of the present disclosure. Of these blood samples 100were determined to be positive for malaria using Giemsa stain based onstandard microscope methodology and 100 being determined to be negative.A duplicate of each of the 200 samples was stained with a dye solutionto have a final concentration in the tested sample of 2 μg/ml AcridineOrange and 15 μg/ml Hoechst 33342 and then analyzed using automatedmachine vision under bright field, UV light and blue light, essentiallyas described above. The results showed that more than 97% of the samplesthat were identified as infected under the conventional method were alsoidentified as such using the AO/Hoechst stain. Out of the 100 samplesthat were deemed healthy using the conventional Giemsa stain, 93 wereconfirmed using the AO/Hoechst stain, but seven samples were identifiedas infected. These seven were then once again analyzed using Giemsareagent (either by repeating both staining and microscopy with a newsample from the same donor or by further microscopy of the originalpreparation which gave rise to the negative result). In all seven casesit was confirmed that indeed they were infected, but apparently at a lowparasitemia of under 1,000 parasites/μl.

The above shows that not only the method disclosed herein allowsdetection (even by machine vision) of infection with high level ofconfidence (above 97%), but also when parasite count is very low (lowparasitemia), even under 1,000 parasites per μl, or under 500 parasitesper μ1 and even at 20 parasites/μ1.

1. Apparatus for use with a blood sample, a first dye that predominantlystains DNA, and a second dye that stains at least one other cellularcomponent being different from DNA, the apparatus comprising: amicroscope system configured to acquire a plurality of images of theblood sample, the microscope system comprising: a first light sourceconfigured to apply brightfield illumination conditions to the bloodsample, while at least one first image of the sample is acquired; asecond light source configured to apply illumination conditions to theblood sample that causes the first dye to fluoresce, while at least onesecond image of the sample is acquired; and a third light sourceconfigured to apply illumination conditions to the blood sample thatcauses the second dye to fluoresce, while at least one third image ofthe sample is acquired; and at least one computer processor configuredto detect an entity within the blood sample, by: identifying a candidateobject within the plurality of images as being a candidate of theentity, by analyzing the first one of the images; identifying that afirst stained area, which is stained by the first dye, is disposedwithin the candidate object, by analyzing the second one of the images;identifying that a second stained area, which is stained by the seconddye, is disposed within the candidate object, by analyzing the third oneof the images; and determining that one or more features of the firstand second stained areas satisfy predetermined criteria associated withthe entity.
 2. The apparatus according to claim 1, wherein identifyingthe first stained area comprises identifying the first stained areabased on an intensity of the first stained area.
 3. The apparatusaccording to claim 1, wherein identifying the first stained areacomprises identifying the first stained area based on a shape of thefirst stained area.
 4. The apparatus according to claim 1, whereinidentifying the first stained area comprises identifying the firststained area based on a consistency of the first stained area.
 5. Theapparatus according to claim 1, wherein the third light source isconfigured to apply illumination conditions to the blood sample thatcauses the second dye to fluoresce while the at least one third image ofthe sample is acquired at a time that is the same as when the secondlight source is configured to apply illumination conditions to the bloodsample that causes the first dye to fluoresce while the at least onesecond image of the sample is acquired.
 6. The apparatus according toclaim 1, wherein the third light source is configured to applyillumination conditions to the blood sample that causes the second dyeto fluoresce while the at least one third image of the sample isacquired at a different time from when the second light sourceconfigured to apply illumination conditions to the blood sample thatcauses the first dye to fluoresce while the at least one second image ofthe sample is acquired.
 7. The apparatus according to claim 1, whereindetermining that one or more features of the first and second stainedareas satisfy predetermined criteria associated with the entitycomprises determining that sizes of the first and second stained areasrelative to a size of the identified object satisfy predeterminedcriteria associated with the entity.
 8. The apparatus according to claim1, wherein determining that one or more features of the first and secondstained areas satisfy predetermined criteria associated with the entitycomprises determining that sizes of the first and second stained areasrelative to each other satisfy predetermined criteria associated withthe entity.
 9. The apparatus according to claim 1, wherein determiningthat one or more features of the first and second stained areas satisfypredetermined criteria associated with the entity comprises determiningthat locations of the first and second stained areas relative to alocation of the identified object satisfy predetermined criteriaassociated with the entity.
 10. The apparatus according to claim 1,wherein determining that one or more features of the first and secondstained areas satisfy predetermined criteria associated with the entitycomprises determining that locations of the first and second stainedareas relative to each other satisfy predetermined criteria associatedwith the entity.
 11. The apparatus according to claim 1, whereindetermining that one or more features of the first and second stainedareas satisfy predetermined criteria associated with the entitycomprises determining that movement of at least one of the first andsecond stained areas satisfies predetermined criteria associated withthe entity.
 12. The apparatus according to claim 1, wherein determiningthat one or more features of the first and second stained areas satisfypredetermined criteria associated with the entity comprises determiningthat intensities of the first and second stained areas satisfypredetermined criteria associated with the entity.
 13. The apparatusaccording to claim 1, wherein determining that one or more features ofthe first and second stained areas satisfy predetermined criteriaassociated with the entity comprises determining that sharpness ofboundaries of the stained areas satisfy predetermined criteriaassociated with the entity.
 14. The apparatus according to claim 1,wherein the at least one computer processor is configured to detect anentity within the blood sample, by detecting a pathogen within thesample.
 15. The apparatus according to claim 1, wherein the at least onecomputer processor is configured to detect an entity within the bloodsample, by detecting a white blood cell within the sample.
 16. Theapparatus according to claim 15, wherein at least one the computerprocessor is configured to identify the white blood cell bydistinguishing between the white blood cell and a pathogen.
 17. Theapparatus according to claim 15, wherein the at least one computerprocessor is configured to identify the white blood cell by determiningthat sizes of the first and second stained areas are similar to that ofthe identified object.
 18. The apparatus according to claim 15, whereinat least one the computer processor is configured to identify the whiteblood cell by determining that sizes of the first and second stainedareas are not substantially smaller than that of the identified object.19. The method according to claim 1, wherein staining the blood samplewith the second dye comprises staining the blood sample with a dye thatstains RNA.
 20. The method according to claim 19, wherein staining theblood sample with the second dye comprises staining the blood samplewith Acridine Orange.